I work on investigating the microbiome of the grapevines Rhizosphere using Shotgun-metagenome sequencing-Illumina. DNA was extracted using PowerSoil® DNA Isolation Kit - QIAGEN and further purified by Sodium acetate. Metagenomic DNA libraries (50 ng input) were prepared using NEBNext® Ultra™ II Prep Kit for Illumina®. The readouts of Bioanalyzer, Qubit™ dsDNA HS, or 16s PCR look perfect. However, the sequencing run gets always underclustered in case of my samples. Nevertheless, it disrupts the clustering of the other samples, too.

I look forward to any help!!